INTRODUCTION TO 

TUBERCULOSIS

GENOTYPING

Facilitator Guide

National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention 

Division of Tuberculosis Elimination
1

Introduction to Tuberculosis Genotyping

Facilitator Guide

Purpose 

 The purpose of the Introduction to Tuberculosis Genotyping slide set is to provide basic education on

tuberculosis (TB) genotyping and how it can be useful in TB prevention and control activities. The 

presentation is estimated to take about 30 minutes.

 This facilitator guide is to be used in conjunction with the Introduction to Tuberculosis Genotyping slide 

set to provide suggested wording to reinforce the messages in the presentation. 

Audience 

 The target audience for the Introduction to Tuberculosis Genotyping slide set is health care 

professionals who have basic or no knowledge of TB genotyping. 

 The target audience for this facilitator guide is faculty and planners who will present the Introduction 

to Tuberculosis Genotyping slide set. 

Acknowledgments 

We wish to thank our colleagues from the Division of Tuberculosis Elimination for their collaboration in 

creating the Introduction to TB Genotyping slide set and facilitator guide.

 From the Communications, Education, and Behavioral Studies Branch 

o Peri Hopkins

o Amera Khan

o Allison Maiuri

o Sarah Segerlind

 From the Surveillance, Epidemiology, and Outbreak Investigations Branch

o Anne Marie France

o Tracie Gardner

o Smita Ghosh

o Juliana Grant 

o Maryam Haddad

o Steve Kammerer

o Lauren Lambert

o Tom Navin
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Slides Speaker Notes

Slide 1

Hi, welcome to today’s presentation.

For the next half hour, I will introduce you to 

tuberculosis (TB) genotyping. 

This course was designed for persons who work 

in the prevention and control of TB and who 

need to have knowledge of TB genotyping. 

Even if you’ve never heard of TB genotyping

before this presentation, that’s ok. This 

presentation is for you.

Slide 2

By the end of this presentation, you will be able 

to 

1. Explain the basics of TB genotyping.

2. Describe how genotyping can be useful 

in TB control.

3. Explain how genotyping results are 

obtained.

We will discuss two case scenarios that 

demonstrate the value that genotyping results 

can add when combined with information 

collected during contact investigations.
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Slide 3

Here is your first quiz question.

What is TB genotyping? 

[ If a clicker system is being used ]

Please enter your choice on the clicker.

Or

[ If no clicker system is being used]

Please raise your hand if you think TB 

genotyping is 

A. A laboratory method to detect if someone 

has TB infection?

Or is it B, a blood test to detect if someone has 

drug-resistant TB? 

Is genotyping C, a laboratory approach that 

analyzes the genetic material, or the DNA, of 

the bacteria that causes TB disease, 

Mycobacterium tuberculosis? 

Do you think it is D, a tool to help understand 

transmission of M. tuberculosis?

Or who thinks the answer is both C and D?

[ Pause for responses ]

Slide 4

**Animated Slide**

The correct answer is E. 

TB genotyping is both • A laboratory test used to analyze the 

genetic material of M. tuberculosis, and 

•A tool to help understand M. 

tuberculosis transmission between 

patients. 

Let’s explore this a little further. [Note to facilitator: If asked about DNA: DNA 

stands for ‘deoxyribonucleic acid’ and is an 

extremely long, double-stranded, nucleic acid 

molecule. DNA carries genes as segments along 

its strands.]
4

Slide 5

TB genotyping can only be done for TB cases 

with positive culture results. The technique 

requires use of material from a culture result.

Genotyping is not possible on negative culture 

results or for persons who have TB infection,

but do not have TB disease.

If M. tuberculosis grows in the culture media, it 

is called an ‘isolate’. 

When two (or more) people have an isolate 

with a matching genotype, that indicates that 

the cases may be related and may be involved 

in the same chain of transmission. 

When two TB patients have isolates with 

nonmatching genotypes, that indicates that 

they are probably not involved in the same 

chain of transmission. 

Slide 6

**Animated Slide**

Genotyping can help us understand 

transmission relationships between persons 

with TB disease.

When one person with TB coughs and 

<<CLICK ONCE>> Transmits the bacteria through the air to 

another person and that person develops TB 

disease, <CLICK TWICE> Their TB bacterium is closely related, and the 

TB DNA will be almost identical. 

<CLICK ONCE>

So we expect genotypes from transmission-

related cases to match, and that may indicate 

that there is a relationship between these 

patients.
5

Slide 7

**Animated Slide**

That may seem complicated, but let’s put it into 

perspective. 

The concept is actually very simple. The 

question is, ‘Do the pictures match?’

TB genotyping is similar to the matching game 

some of us may have played as kids. Basically,

we’re looking for matches among all the 

pictures, or genotype results, we have. 

So here, we have two groups of matching frogs, 

the green group and 

<CLICK ONCE>

the orange group.

<CLICK ONCE>

And then there are a few outliers. 

Which ones are not like the others? Right, the 

last two in the first column and the turquoise 

and black spotted frog in the top right corner.

Slide 8

**Animated Slide**

In TB genotyping, we’re looking for groups of 

matching genotypes, or clusters. 

So here we have two clusters, 

<CLICK ONCE>

a purple one, and 

<CLICK ONCE>

a teal one. 

When two or more M. tuberculosis isolates 

match by genotype, they are referred to as a 

“genotype cluster.” 

A “cluster” means that the cases may be 

transmission-related.
6

Slide 9

How can genotyping be useful in TB control? 

TB genotyping can be beneficial in multiple 

ways. 

First, TB genotyping can help in conventional TB 

contact investigations by • Confirming that TB cases linked by 

contact investigation are related by 

transmission, and 

•Refuting or disproving TB case 

connections. If the genotypes do not match, the TB cases 

that may seem to be linked by contact 

investigation results are not actually linked by 

transmission. 

TB genotyping can also help us find previously 

unidentified contacts and other TB case 

connections. 

This could lead to the identification of • A previously unknown source case, and • Other locations where transmission may

have occurred. 

 

One of the major uses of TB genotyping is to 

help us detect and prevent outbreaks. By 

improved knowledge of how cases are linked 

and identifying infected contacts, you can 

prevent additional cases from occurring.

As mentioned, clusters of TB cases with 

matching genotypes may be related by recent 

transmission.

Genotyping can help refute outbreaks when a 

group of cases is suspected to be related by 

traditional epidemiology, but the genotypes do 

not match, which tells us that the cases do not 

actually represent an outbreak. 
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Slide 10

Additionally, for a patient who is presenting 

with a second episode of TB disease, we can 

look at the genotypes to see if they are the 

same as when they were first diagnosed or 

different, thus helping to distinguish between a 

relapse and new infection. 

Another advantage of genotyping is that an 

incorrect TB diagnosis based on a false-positive 

culture result will be identified more quickly.

False-positive culture results can be caused by

various errors:

• Cross-contamination in the lab,

• Contamination of a clinical device, such 

as a bronchoscope, or

• Mislabeling of a specimen or other 

documentation errors.

Consequences of false-positive TB culture 

results include incorrect TB diagnosis and 

unnecessary treatment and wasted public 

health resources.

Through these different applications, TB 

genotyping 

• Allows for a more comprehensive 

understanding of contact investigation 

results,

• Can prevent new TB cases, 

• Distinguishes relapse of previous TB 

from a new infection, and

• Saves time and public health resources 

when a situation is determined not to 

be an outbreak.
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Slide 11

**Animated Slide**

Let’s start with a pretty common case scenario: 

A local TB program is monitoring genotype 

results in their jurisdiction, say County A, and 

within a 4-month period, three people in the 

same town are diagnosed with TB. 

<CLICK ONCE>

Two are members of a family: a mother and a 

6-year old son. 

<CLICK ONCE>

One other person, a neighbor, said she spent 

much of her time at that house during the day. 

<CLICK ONCE>

So the conclusion of our epidemiologic 

investigation is that all three of the persons 

with TB spent most of their time together at 

the same house, 

<CLICK ONCE>

And because of this, we strongly suspect that 

these three cases are related.

Slide 12

Here are the genotype results for the three 

patients linked to this household. 

We can see that TB bacteria from all of these 

patients had the same genotype result. 

How would you interpret these genotype 

results?
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Slide 13

The interpretation would likely be that, 

because we know that genotype results from 

all three cases matched, And we know the mother, her son, and the 

neighbor all spent time together in that house 

and shared the same air space, We assume that these three cases were likely 

related by transmission.

Slide 14

**Animated Slide**

Let’s go back to the household and take a 

closer look at those cases. 

The contact investigation activities for the 

mother did not find any other cases of active 

TB disease. 

There were two other people in the household, 

<CLICK ONCE>

An adult male and a 7-year old girl. They both 

received a TB skin test, and both were 

diagnosed with TB infection (indicated as pink). 

They were started on the 12-dose regimen of 

isoniazid and rifapentine one time a week by 

directly observed therapy at their home. 

During interviews with the neighbor, she did 

not name any additional contacts outside of 

this household and said she lived alone.

So, all in all, a fairly neat little scenario, and we 

think we’re done, right?

Maybe not. Does anyone have any concerns 

about this situation?

Could there possibly be unnamed contacts?
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Slide 15

Yes, there could be more contacts and there 

could be more cases. 

In fact, when County A looked at all cases with 

Genotype 1 in their jurisdiction during 2013, 

this is the list they discovered.

We already knew about the two family 

members and their neighbor. 

But there are two other TB cases with this 

same genotype, Patient A and Patient B.

What does genotyping tell us here?

Slide 16

The genotype results show that the five cases 

all had matching genotypes within one year, so 

they may all be related by transmission.

But we don’t know the time or locations where 

transmission may have occurred for Patients A 

and B. 

It’s possible that they were infected many years 

ago, but it’s also possible that they have been 

recently infected. 

We need more information to try to determine 

if Patients A and B may be related by 

transmission to each other and to the other TB 

cases. 
11

Slide 17

Our next steps would be to investigate further. 

If Patient A and Patient B are related in some 

way to each other or to the rest of the patients 

in the cluster (for example, if they attended the 

same social club that the mother attended), we 

may be able to identify 

• Other potential locations of 

transmission, and

• Missed contacts who need testing. 

To do this, we can do a careful review of 

• Public health records,

• Contact investigation logs,

• Estimated infectious periods of the 

cases, and 

• Information from interviews with TB 

cases and contacts in the genotype 

cluster.

Slide 18

**Animated Slide**

Now for the second case scenario.

We’re in a different state now; one that has 

legal gambling. 

Within a single month, three women are 

diagnosed with TB. 

All three women work in the same casino, and 

they all work the nightshift together. 

Additionally, one woman’s boyfriend is also 

diagnosed with TB.

<CLICK ONCE>
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Slide 19

Do you think these TB cases are related by 

transmission?

[ If a clicker is being used ]

If you think yes, press A on your clicker. 

If no, press, B. 

If you think that maybe they are related by 

transmission, press C. 

[ If no clicker is being used ]

Raise your hand if you think the answer is 

• Yes?

• No?

• Maybe?

[ Pause for responses ]

Slide 20

**Animated Slide**

If you answered C, you are correct. 

These TB cases may be related by transmission.

But to determine that, we need more 

information. 
13

Slide 21

Here are the genotype results for those four TB 

cases. 

The TB bacteria cultured from Employee 1 was 

genotype number 2. 

The TB bacterium from employee 2 was a 

different genotype, genotype number 3. 

Employee 3 had genotype number 4, and 

The boyfriend’s genotype was number 5. 

How would you interpret these results?

Slide 22

[ If a clicker system is being used ]

Please enter your choice on the clicker.

Or

[ If no clicker system is being used ]

Who thinks:

A. The genotype data are wrong

B. The genotype data could be wrong, 

since there’s epidemiologic information 

that they’re connected by transmission

C. These cases are not related by 

transmission, or 

D. Who knows?

[ Pause for responses ]
14

Slide 23

**Animated Slide**

The correct answer is ‘C’. 

These cases are not related by transmission. 

How do we know that?

[ Pause for responses ]

Slide 24

**Animated Slide**

The genotype results from each of these cases 

were different. 

That tells us that these cases are not related by 

transmission. 

Finding TB in four TB cases who happened to 

have had social connections was a coincidence. 

Rather than an outbreak investigation, this 

situation calls for four simultaneous contact 

investigations, with three in the same work 

site. 

<CLICK ONCE>

This is NOT an outbreak at this point, and that 

is great news.

However, it is possible that future contact 

investigation activities uncover previously 

undetected cases. 
15

Slide 25

**Animated Slide**

Now that you’ve seen how genotyping results 

can be used in a TB program, you may be 

wondering how genotyping results are 

obtained.

First, a person with suspected or confirmed TB 

provides a ‘specimen.’

A specimen is a clinical sample (e.g., sputum, 

bronchial wash, urine, blood, cerebrospinal 

fluid, or tissues from organs or gastric 

aspirates). 

Then the specimen is sent to a laboratory 

(hospital, private, or state lab) for culturing. 

If M. tuberculosis grows in the culture media, it 

is called an ‘isolate’. 

Only isolates identified as M. tuberculosis can 

be genotyped.

Then, the isolate goes to a genotyping 

laboratory for testing and identification. 
16

Slide 26

In conclusion, we have shared a lot of 

information with you about TB genotyping. 

But the two main take home points are:

First, genotyping can be a useful tool in TB 

control in multiple ways, including 

• Helping to find previously unidentified

or unnamed contacts, 

• Detecting and preventing outbreaks (for 

example, when a TB culture result is 

identified as being false-positive), and 

• Refuting outbreaks.

When a suspected outbreak is refuted by 

genotyping, TB programs can save time and 

resources. 

While a contact investigation for each TB case 

will be required, additional activities related to 

outbreak investigation and response will not be 

necessary.

The second take home point is that interpreting 

genotyping results can be as simple as, “Do the 

pictures match?”

If yes, the cases may be related by 

transmission, and additional investigation may 

be warranted. 

If the pictures don’t match, the cases are not 

likely related by transmission, thus determining 

that it is not an outbreak, and further 

investigation activities may be avoided.
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Slide 27

This presentation is an introduction about 

genotyping and how it can be helpful to TB 

control. There is a lot more practical 

information out there to help programs 

interested in learning more and applying 

genotyping to their own TB control efforts.

Various resources are posted on the CDC 

Division of Tuberculosis Elimination website 

under genotyping, and additional resources are 

being developed.

You can access the TB Genotyping Best 

Practices document, which is a consensus 

document developed by CDC in collaboration 

with multiple state and local TB programs. This document describes specific steps and actions 

in applying TB genotyping effectively. 

The Tuberculosis Genotyping Information 

System, or TB GIMS, is a web-based system that 

stores and manages genotyping data on TB 

patients in the United States. 

Also, you can email CDC at 

tbgenotyping@cdc.gov

For local programs, your state genotyping 

program should be the first place to go for 

more information. We’re happy to help you 

connect with them if you don’t know who to 

contact.

Slide 28

Thank you very much for your interest. 

I’m happy to try to answer any questions you 

may have at this time.
CS259382-A